Resolve "Migrate some material on Configurations from NEMO book to User guide"

source/cfgs.rst

@@ -2,24 +2,16 @@
 Run the Reference configurations
 ################################
 
-.. note::
-
-   Lack of illustrations for ref. cfgs, and more generally in the guide.
-
 NEMO is distributed with a set of reference configurations allowing both
 the user to set up his own first applications and
 the developer to test/validate his NEMO developments (using SETTE package).
 
 .. contents::
    :local:
-   :depth: 1
 
 .. attention::
 
-   Concerning the configurations,
-   the NEMO System Team is only in charge of the "Reference Configurations" described below.
-
-.. hint::
+   Please note that the NEMO System Team is only in charge of the maintenance of the "Reference Configurations" described below.
 
    Configurations developed by external research projects or initiatives that
    make use of NEMO are welcome to be publicized through the website by
@@ -105,20 +97,22 @@ a split explicit free surface scheme.
 AMM12
 -----
 
-``AMM12`` stands for *Atlantic Margin Model at 12 km* that is
-a regional configuration covering the Northwest European Shelf domain on
-a regular horizontal grid of ~12 km of resolution (see :cite:`o’dea.arnold.ea_JOO12`).
+The AMM, Atlantic Margins Model, is a regional model covering the Northwest European Shelf domain on
+a regular lat-lon grid at approximately 12km horizontal resolution  (see :cite:`o’dea.arnold.ea_JOO12`).
+
+The appropriate ``&namcfg`` namelist, used to build the correct dimensions of the AMM domain, is available at ``./cfgs/AMM12/EXPREF/namelist_cfg``
 
 .. image:: _static/AMM_domain.png
    :align: center
 
-This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.
-In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme,
-tidal lateral boundary conditions using a flather scheme (see more in ``BDY``).
+This configuration allows to tests several features of NEMO functionality specifically addressed to the shelf seas.
+In particular, ``AMM12`` uses the vertical s-coordinates system, GLS turbulence scheme (``ln_zdfgls=.true.``),
+and tidal lateral boundary conditions using a flather scheme (see more in ``BDY``).
+
 Boundaries may be completely omitted by setting ``ln_bdy = .false.`` in ``nambdy``.
 
 Sample surface fluxes, river forcing and an initial restart file are included to test a realistic model run
-(``AMM12_v4.2.0.tar``).
+(see ``AMM12_v4.2.0.tar`` in the table).
 
 Note that, the Baltic boundary is included within the river input file and is specified as a river source,
 but unlike ordinary river points the Baltic inputs also include salinity and temperature data.
@@ -126,14 +120,15 @@ but unlike ordinary river points the Baltic inputs also include salinity and tem
 C1D_PAPA
 --------
 
+This 1D model option simulates a stand alone water column for the `PAPA station`_ located in
+the northern-eastern Pacific Ocean at 50.1°N, 144.9°W.
+See `Reffray et al. (2015) <https://gmd.copernicus.org/articles/8/69/2015/>`_ for the description of
+its physical and numerical turbulent-mixing behaviour.
+
 .. image:: _static/Papa2015.jpg
    :height: 90px
    :align:  center
 
-``C1D_PAPA`` is a 1D configuration for the `PAPA station`_ located in
-the northern-eastern Pacific Ocean at 50.1°N, 144.9°W.
-See `Reffray et al. (2015) <https://gmd.copernicus.org/articles/8/69/2015/>`_ for the description of
-its physical and numerical turbulent-mixing behaviour.
 
 | The water column setup, called NEMO1D, is activated by  
   setting ``ln_c1d = .true.`` in ``namdom`` and
@@ -150,6 +145,18 @@ Input files in C1D_v4.2.0.tar: forcing_PAPASTATION_1h_y201[0-1].nc:
   observed data and Levitus 2009 climatology,and
   chlorophyll_PAPASTATION.nc: surface chlorophyll file from Seawifs data
 
+The 1D model is a very useful tool to:
+
+- learn about the physics and numerical treatment of vertical mixing processes;
+
+- investigate suitable parameterisations of unresolved turbulence (surface wave breaking, Langmuir circulation, ...);
+
+- compare the behaviour of different vertical mixing schemes;
+
+- perform sensitivity studies on the vertical diffusion at a particular point of an ocean domain;
+
+- produce extra diagnostics, without the large memory requirement of the full 3D model.
+
 
 GYRE_PISCES
 -----------

source/tests.rst

@@ -208,6 +208,10 @@ C1D_PAPA
 --------
 
 1d (vertical) test case at the PAPA station located in the North Pacific Ocean. This buoy is located in a region of weak horizontal advection and is commonly used by the community to validate turbulent closures (see :cite:`reffray_GMD15`).
+
+For a more extensice description of this configuration please refer to the Reference Configurations section
+
+
  
 STATION_ASF
 -----------